off-topic: "special" format for multiple sequence (protein) alignment

From: WENHE ZHONG
Date: 3 February 2012 05:32
Dear members,

Apologize for this off-topic question. I am looking for a protein sequence alignment tool which is capable to generate a particular output file similar to the attached format (please see the attached picture). I have been looking at some popular programs but none of them can show the conserved amino acids by colored blocks as shown in the attached file.

Maybe some of you have seen some programs can do this? Thank you.







King regards,
Wenhe

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From: Ethan Merritt

That looks similar to the output of TeXshade, with the shading
mode set to "hydropathy".

       Ethan

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From: Sebastiano Pasqualato

Dear Wenhe,

have you looked at http://www.jalview.org/ ?

is this what you are looking for? http://www.jalview.org/examples/examples3.html

ciao,

Sebastiano

<alignment.png>

-- Sebastiano Pasqualato,

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From: David Briggs
I'm pretty certain that Jalview http://www.jalview.org/ can do that
(you might have to set the user defined colours yourself).

Dave.


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From: Tim Gruene

Dear Wenhe,

clustalx exports to PostScript with colour coding according to
conservation. seaview is another tool for that purpose.

Tim

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From: Navdeep Sidhu
Dear Wenhe:

Indonesia (Madsen, Johansson & Kleywegt, 2002), <http://xray.bmc.uu.se/~dennis/>, also has multiple coloring and output format possibilities, including postscript, similar to your example. Ten years later, it's still easy to install and run (tested on Fedora Linux in the past month). Apart from the package itself, you just need to install Java Runtime Environment and give the input sequences in PIR format.

Regards,
Navdeep


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From: Schubert, Carsten [JRDUS]

Wenhe,

Bioedit (http://www.mbio.ncsu.edu/bioedit/bioedit.html)  is able to do this. You can also export a nice alignment as RTF file into Word from the graphics view. This comes in handy for publication and presentation.

Cheers,

                Carsten

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From: Christian Roth

Hi Wenhe,

if you have already your alignment file you could also load it in Charlie Bonds
"ALINE".
The program allows to color by similarity in grayscale as well as in colour
mode.

Regards

Christian

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From: Francisco Hernandez-Guzman

Hello Wenhe,

Have you tried using our free Discovery Studio Visualizer?

http://accelrys.com/products/discovery-studio/visualization-download.php

You can generate and color alignments using various properties like alignment similarity, chemical type, steric, and many others. In addition, you can select your own custom coloring for each property.

I have attached a small screenshot of the view for your sample picture trying to match your coloring scheme.

Cheers,

Francisco